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Add NCI-CRDC TCGA and CPTAC studies to news release #10910

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merged 6 commits into from
Aug 1, 2024
Merged

Add NCI-CRDC TCGA and CPTAC studies to news release #10910

merged 6 commits into from
Aug 1, 2024

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rmadupuri
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Updated the news release to include the 33 TCGA and 10 CPTAC datasets from GDC.

jamesqo
jamesqo requested changes Jul 25, 2024
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docs/News.md Outdated
* [Thymoma (TCGA, GDC)](https://www.cbioportal.org/study/summary?id=thym_tcga_gdc) *124 samples*
* [Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor (TCGA, GDC)](https://www.cbioportal.org/study/summary?id=ucs_tcga_gdc) *57 samples*
* [Uveal Melanoma (TCGA, GDC)](https://www.cbioportal.org/study/summary?id=um_tcga_gdc) *80 samples*
* [Breast (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=breast_cptac_gdc) *154 samples*
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Suggested change
* [Breast (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=breast_cptac_gdc) *154 samples*
* [Breast Cancer (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=breast_cptac_gdc) *154 samples*

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^ Niki had mentioned that he prefers " Cancer" instead of "", so I will be updating the names of the studies accordingly. See the discussion in #data-feedback: https://cbioportal.slack.com/archives/C04PHKPKF2R/p1721693960892619?thread_ts=1721329662.398769&cid=C04PHKPKF2R

docs/News.md Outdated
* [Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor (TCGA, GDC)](https://www.cbioportal.org/study/summary?id=ucs_tcga_gdc) *57 samples*
* [Uveal Melanoma (TCGA, GDC)](https://www.cbioportal.org/study/summary?id=um_tcga_gdc) *80 samples*
* [Breast (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=breast_cptac_gdc) *154 samples*
* [CNS/Brain (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=brain_cptac_gdc) *74 samples*
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* [CNS/Brain (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=brain_cptac_gdc) *74 samples*
* [CNS/Brain Cancer (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=brain_cptac_gdc) *74 samples*

docs/News.md Outdated
* [Head and Neck Carcinoma, Other (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=ohnca_cptac_gdc) *150 samples*
* [Lung Adenocarcinoma (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=luad_cptac_gdc) *180 samples*
* [Lung Squamous Cell Carcinoma (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=lusc_cptac_gdc) *90 samples*
* [Ovary/Fallopian Tube (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=ovary_cptac_gdc) *113 samples*
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* [Ovary/Fallopian Tube (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=ovary_cptac_gdc) *113 samples*
* [Ovarian Cancer (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=ovary_cptac_gdc) *113 samples*

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Not 100% sure about this one since I am removing Fallopian Tube, but this sounds smoother than Ovary/Fallopian Tube Cancer. Additionally, none of the existing studies we have on the ovary mention the fallopian tube. Thoughts?

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That makes sense. Lets have it as Ovarian Cancer to be consistent with other studies.

docs/News.md Outdated
* [Lung Adenocarcinoma (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=luad_cptac_gdc) *180 samples*
* [Lung Squamous Cell Carcinoma (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=lusc_cptac_gdc) *90 samples*
* [Ovary/Fallopian Tube (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=ovary_cptac_gdc) *113 samples*
* [Pancreas (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=pancreas_cptac_gdc) *139 samples*
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Suggested change
* [Pancreas (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=pancreas_cptac_gdc) *139 samples*
* [Pancreatic Cancer (CPTAC, GDC)](https://www.cbioportal.org/study/summary?id=pancreas_cptac_gdc) *139 samples*

docs/News.md Outdated
@@ -1,3 +1,49 @@
## July 29, 2024
* **Added data** consisting of 12,863 samples from 33 TCGA and 10 CPTAC studies from the GDC as part of the NCI-CRDC initiative. The studies are generated though the [ISB-CGC](https://portal.isb-cgc.org/) BigQuery tables.
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Should we expand the acronyms and/or link out, in case users aren't familiar with them?

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Also, Ben wants to link out directly to the subpage with BigQuery tables rather than the landing page of the ISB-CGC site.

Suggested change
* **Added data** consisting of 12,863 samples from 33 TCGA and 10 CPTAC studies from the GDC as part of the NCI-CRDC initiative. The studies are generated though the [ISB-CGC](https://portal.isb-cgc.org/) BigQuery tables.
* **Added data** consisting of 12,863 samples from 33 TCGA and 10 CPTAC studies from the [Genomic Data Commons (GDC)](https://gdc.cancer.gov) as part of the [Cancer Research Data Commons (NCI-CRDC)](https://datacommons.cancer.gov) initiative. The studies are generated through the [ISB-CGC BigQuery tables](https://bq-search.isb-cgc.org/search?status=current).

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Thanks for the review. Updated.

rmadupuri
rmadupuri commented Jul 25, 2024
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docs/News.md Outdated
* [Prostate Adenocarcinoma (TCGA, GDC)](https://www.cbioportal.org/study/summary?id=prad_tcga_gdc) *501 samples*
* [Rectal Adenocarcinoma (TCGA, GDC)](https://www.cbioportal.org/study/summary?id=read_tcga_gdc) *171 samples*
* [Renal Clear Cell Carcinoma (TCGA, GDC)](https://www.cbioportal.org/study/summary?id=ccrcc_tcga_gdc) *537 samples*
* [Soft Tissue (TCGA, GDC)](https://www.cbioportal.org/study/summary?id=soft_tissue_tcga_gdc) *264 samples*
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@jamesqo, should this also be Soft Tissue Cancer?

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@rmadupuri Ah yes, good catch!

n1zea144
n1zea144 requested changes Jul 29, 2024
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docs/News.md Outdated
@@ -1,3 +1,49 @@
## July 29, 2024
* **Added data** consisting of 12,863 samples from 33 TCGA and 10 CPTAC studies from the [Genomic Data Commons (GDC)](https://gdc.cancer.gov) as part of the [Cancer Research Data Commons (NCI-CRDC)](https://datacommons.cancer.gov) initiative. The studies are generated through the [ISB-CGC BigQuery tables](https://bq-search.isb-cgc.org/search?status=current).
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@n1zea144 n1zea144 Jul 29, 2024 •
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Can we change the last sentence to "More information can be found on our FAQ" and link to this page
https://docs.cbioportal.org/user-guide/faq/#tcga

...assuming this will be link to new content in @jamesqo PR
https://github.com/cBioPortal/cbioportal/blob/699e939482228c55321afad3fd9ee9c237949cf9/docs/user-guide/faq.md#tcga

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Thanks @n1zea144! Updated.

@rmadupuri rmadupuri changed the title Add GDC studies to news release Add NCI-CRDC studies to news release Jul 29, 2024
@rmadupuri rmadupuri changed the title Add NCI-CRDC studies to news release Add NCI-CRDC TCGA and CPTAC studies to news release Jul 29, 2024
inodb
inodb approved these changes Aug 1, 2024
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Yay 🏆 !

@inodb inodb merged commit ee2736e into master Aug 1, 2024
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@inodb inodb deleted the update_news branch August 1, 2024 20:49
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sonarcloud bot commented Aug 1, 2024

Quality Gate Passed Quality Gate passed

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0.0% Duplication on New Code

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@rmadupuri @n1zea144 @inodb @jamesqo